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https://www.readbyqxmd.com/read/28812986/epigenome-aberrations-emerging-driving-factors-of-the-clear-cell-renal-cell-carcinoma
#1
REVIEW
Ali Mehdi, Yasser Riazalhosseini
Clear cell renal cell carcinoma (ccRCC), the most common form of Kidney cancer, is characterized by frequent mutations of the von Hippel-Lindau (VHL) tumor suppressor gene in ~85% of sporadic cases. Loss of pVHL function affects multiple cellular processes, among which the activation of hypoxia inducible factor (HIF) pathway is the best-known function. Constitutive activation of HIF signaling in turn activates hundreds of genes involved in numerous oncogenic pathways, which contribute to the development or progression of ccRCC...
August 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28812720/antagonistic-pleiotropy-and-mutation-accumulation-influence-human-senescence-and-disease
#2
Juan Antonio Rodríguez, Urko M Marigorta, David A Hughes, Nino Spataro, Elena Bosch, Arcadi Navarro
Senescence has long been a public health challenge as well as a fascinating evolutionary problem. There is neither a universally accepted theory for its ultimate causes, nor a consensus about what may be its impact on human health. Here we test the predictions of two evolutionary explanations of senescence-mutation accumulation and antagonistic pleiotropy-which postulate that genetic variants with harmful effects in old ages can be tolerated, or even favoured, by natural selection at early ages. Using data from genome-wide association studies (GWAS), we study the effects of genetic variants associated with diseases appearing at different periods in life, when they are expected to have different impacts on fitness...
January 30, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812654/transitions-between-phases-of-genomic-differentiation-during-stick-insect-speciation
#3
Rüdiger Riesch, Moritz Muschick, Dorothea Lindtke, Romain Villoutreix, Aaron A Comeault, Timothy E Farkas, Kay Lucek, Elizabeth Hellen, Víctor Soria-Carrasco, Stuart R Dennis, Clarissa F de Carvalho, Rebecca J Safran, Cristina P Sandoval, Jeff Feder, Regine Gries, Bernard J Crespi, Gerhard Gries, Zach Gompert, Patrik Nosil
Speciation can involve a transition from a few genetic loci that are resistant to gene flow to genome-wide differentiation. However, only limited data exist concerning this transition and the factors promoting it. Here, we study phases of speciation using data from >100 populations of 11 species of Timema stick insects. Consistent with early phases of genic speciation, adaptive colour-pattern loci reside in localized genetic regions of accentuated differentiation between populations experiencing gene flow...
February 17, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812610/genome-wide-interrogation-advances-resolution-of-recalcitrant-groups-in-the-tree-of-life
#4
Dahiana Arcila, Guillermo Ortí, Richard Vari, Jonathan W Armbruster, Melanie L J Stiassny, Kyung D Ko, Mark H Sabaj, John Lundberg, Liam J Revell, Ricardo Betancur-R
Much progress has been achieved in disentangling evolutionary relationships among species in the tree of life, but some taxonomic groups remain difficult to resolve despite increasing availability of genome-scale data sets. Here we present a practical approach to studying ancient divergences in the face of high levels of conflict, based on explicit gene genealogy interrogation (GGI). We show its efficacy in resolving the controversial relationships within the largest freshwater fish radiation (Otophysi) based on newly generated DNA sequences for 1,051 loci from 225 species...
January 13, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812581/nfia-co-localizes-with-ppar%C3%AE-and-transcriptionally-controls-the-brown-fat-gene-program
#5
Yuta Hiraike, Hironori Waki, Jing Yu, Masahiro Nakamura, Kana Miyake, Gaku Nagano, Ryo Nakaki, Ken Suzuki, Hirofumi Kobayashi, Shogo Yamamoto, Wei Sun, Tomohisa Aoyama, Yusuke Hirota, Haruya Ohno, Kenji Oki, Masayasu Yoneda, Andrew P White, Yu-Hua Tseng, Aaron M Cypess, Therese J Larsen, Naja Z Jespersen, Camilla Scheele, Shuichi Tsutsumi, Hiroyuki Aburatani, Toshimasa Yamauchi, Takashi Kadowaki
Brown fat dissipates energy as heat and protects against obesity. Here, we identified nuclear factor I-A (NFIA) as a transcriptional regulator of brown fat by a genome-wide open chromatin analysis of murine brown and white fat followed by motif analysis of brown-fat-specific open chromatin regions. NFIA and the master transcriptional regulator of adipogenesis, PPARγ, co-localize at the brown-fat-specific enhancers. Moreover, the binding of NFIA precedes and facilitates the binding of PPARγ, leading to increased chromatin accessibility and active transcription...
August 14, 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28812568/gene-expression-plasticity-as-a-mechanism-of-coral-adaptation-to-a-variable-environment
#6
Carly D Kenkel, Mikhail V Matz
Local adaptation is ubiquitous, but the molecular mechanisms that give rise to this ecological phenomenon remain largely unknown. A year-long reciprocal transplant of mustard hill coral (Porites astreoides) between a highly environmentally variable inshore habitat and a more stable offshore habitat demonstrated that populations exhibit phenotypic signatures that are consistent with local adaptation. We characterized the genomic basis of this adaptation in both coral hosts and their intracellular symbionts (Symbiodinium sp...
November 7, 2016: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812221/multimodal-neuroimaging-in-schizophrenia-description-and-dissemination
#7
C J Aine, H J Bockholt, J R Bustillo, J M Cañive, A Caprihan, C Gasparovic, F M Hanlon, J M Houck, R E Jung, J Lauriello, J Liu, A R Mayer, N I Perrone-Bizzozero, S Posse, J M Stephen, J A Turner, V P Clark, Vince D Calhoun
In this paper we describe an open-access collection of multimodal neuroimaging data in schizophrenia for release to the community. Data were acquired from approximately 100 patients with schizophrenia and 100 age-matched controls during rest as well as several task activation paradigms targeting a hierarchy of cognitive constructs. Neuroimaging data include structural MRI, functional MRI, diffusion MRI, MR spectroscopic imaging, and magnetoencephalography. For three of the hypothesis-driven projects, task activation paradigms were acquired on subsets of ~200 volunteers which examined a range of sensory and cognitive processes (e...
August 15, 2017: Neuroinformatics
https://www.readbyqxmd.com/read/28812021/association-analysis-of-arsenic-induced-straighthead-in-rice-oryza-sativa-l-based-on-the-selected-population-with-a-modified-model
#8
Xiaobai Li, Biaolin Hu, Xuhao Pan, Ning Zhang, Dianxing Wu
A rice physiological disorder makes mature panicle keep erect with empty grains termed as "straighthead." Straighthead causes yield losses and is a serious threat to rice production worldwide. Here, a new study of association mapping was conducted to identify QTL involved in straighthead. A subset of 380 accessions was selected from the USDA rice core collection and genotyped with 72 genome-wide SSR markers. An optimal model implemented with principle components (PCs) was used in this association mapping. As a result, five markers were identified to be significantly associated with straighthead...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28811844/lsd1-dual-function-in-mediating-epigenetic-corruption-of-the-vitamin-d-signaling-in-prostate-cancer
#9
Sebastiano Battaglia, Ellen Karasik, Bryan Gillard, Jennifer Williams, Trisha Winchester, Michael T Moser, Dominic J Smiraglia, Barbara A Foster
BACKGROUND: Lysine-specific demethylase 1A (LSD1) is a key regulator of the androgen (AR) and estrogen receptors (ER), and LSD1 levels correlate with tumor aggressiveness. Here, we demonstrate that LSD1 regulates vitamin D receptor (VDR) activity and is a mediator of 1,25(OH)2-D3 (vitamin D) action in prostate cancer (PCa). METHODS: Athymic nude mice were xenografted with CWR22 cells and monitored weekly after testosterone pellet removal. Expression of LSD1 and VDR (IHC) were correlated with tumor growth using log-rank test...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28811740/multiple-testing-in-the-context-of-gene-discovery-in-sickle-cell-disease-using-genome-wide-association-studies
#10
Kevin H M Kuo
The issue of multiple testing, also termed multiplicity, is ubiquitous in studies where multiple hypotheses are tested simultaneously. Genome-wide association study (GWAS), a type of genetic association study that has gained popularity in the past decade, is most susceptible to the issue of multiple testing. Different methodologies have been employed to address the issue of multiple testing in GWAS. The purpose of the review is to examine the methodologies employed in dealing with multiple testing in the context of gene discovery using GWAS in sickle cell disease complications...
2017: Genomics Insights
https://www.readbyqxmd.com/read/28811569/transcriptional-response-to-stress-is-pre-wired-by-promoter-and-enhancer-architecture
#11
Anniina Vihervaara, Dig Bijay Mahat, Michael J Guertin, Tinyi Chu, Charles G Danko, John T Lis, Lea Sistonen
Programs of gene expression are executed by a battery of transcription factors that coordinate divergent transcription from a pair of tightly linked core initiation regions of promoters and enhancers. Here, to investigate how divergent transcription is reprogrammed upon stress, we measured nascent RNA synthesis at nucleotide-resolution, and profiled histone H4 acetylation in human cells. Our results globally show that the release of promoter-proximal paused RNA polymerase into elongation functions as a critical switch at which a gene's response to stress is determined...
August 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28811563/crosstalk-between-diurnal-rhythm-and-water-stress-reveals-an-altered-primary-carbon-flux-into-soluble-sugars-in-drought-treated-rice-leaves
#12
Seo-Woo Kim, Sang-Kyu Lee, Hee-Jeong Jeong, Gynheung An, Jong-Seong Jeon, Ki-Hong Jung
Plants retain rhythmic physiological responses when adapting to environmental challenges. However, possible integrations between drought conditions and those responses have not received much focus, especially regarding crop plants, and the relationship between abiotic stress and the diurnal cycle is generally not considered. Therefore, we conducted a genome-wide analysis to identify genes showing both diurnal regulation and water-deficiency response in rice (Oryza sativa). Among the 712 drought-responsive genes primary identified, 56...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811542/identification-replication-and-characterization-of-epigenetic-remodelling-in-the-aging-genome-a-cross-population-analysis
#13
Shuxia Li, Lene Christiansen, Kaare Christensen, Torben A Kruse, Paul Redmond, Riccardo E Marioni, Ian J Deary, Qihua Tan
Aging is a complex biological process regulated by multiple cellular pathways and molecular mechanisms including epigenetics. Using genome-wide DNA methylation data measured in a large collection of Scottish old individuals, we performed discovery association analysis to identify age-methylated CpGs and replicated them in two independent Danish cohorts. The double-replicated CpGs were characterized by distribution over gene regions and location in relation to CpG islands. The replicated CpGs were further characterized by involvement in biological pathways to study their functional implications in aging...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811496/genome-wide-expression-differences-in-anti-vegf-and-dexamethasone-treatment-of-inflammatory-angiogenesis-in-the-rat-cornea
#14
Pierfrancesco Mirabelli, Anthony Mukwaya, Anton Lennikov, Maria Xeroudaki, Beatrice Peebo, Mira Schaupper, Neil Lagali
Angiogenesis as a pathological process in the eye can lead to blindness. In the cornea, suppression of angiogenesis by anti-VEGF treatment is only partially effective while steroids, although effective in treating inflammation and angiogenesis, have broad activity leading to undesirable side effects. In this study, genome-wide expression was investigated in a suture-induced corneal neovascularization model in rats, to investigate factors differentially targeted by dexamethasone and anti-Vegf. Topical treatment with either rat-specific anti-Vegf, dexamethasone, or normal goat IgG (sham) was given to sutured corneas for 48 hours, after which in vivo imaging, tissue processing for RNA microarray, and immunofluorescence were performed...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811387/selection-constrains-high-rates-of-tandem-repetitive-dna-mutation-in-daphnia-pulex
#15
Jullien M Flynn, Ian Caldas, Melania E Cristescu, Andrew G Clark
A long-standing evolutionary puzzle is that all eukaryotic genomes contain large amounts of tandemly-repeated DNA whose sequence motifs and abundance vary greatly among even closely related species. To elucidate the evolutionary forces governing tandem repeat dynamics, quantification of the rates and patterns of mutations in repeat copy number and tests of its selective neutrality are necessary. Here we used whole-genome sequences of 28 mutation accumulation (MA) lines of Daphnia pulex in addition to six isolates from a non-MA population originating from the same progenitor to both estimate mutation rates of abundances of repeat sequences and evaluate the selective regime acting upon them...
August 15, 2017: Genetics
https://www.readbyqxmd.com/read/28811376/in-vivo-loss-of-function-screens-identify-kpnb1-as-a-new-druggable-oncogene-in-epithelial-ovarian-cancer
#16
Michiko Kodama, Takahiro Kodama, Justin Y Newberg, Hiroyuki Katayama, Makoto Kobayashi, Samir M Hanash, Kosuke Yoshihara, Zhubo Wei, Jean C Tien, Roberto Rangel, Kae Hashimoto, Seiji Mabuchi, Kenjiro Sawada, Tadashi Kimura, Neal G Copeland, Nancy A Jenkins
Epithelial ovarian cancer (EOC) is a deadly cancer, and its prognosis has not been changed significantly during several decades. To seek new therapeutic targets for EOC, we performed an in vivo dropout screen in human tumor xenografts using a pooled shRNA library targeting thousands of druggable genes. Then, in follow-up studies, we performed a second screen using a genome-wide CRISPR/Cas9 library. These screens identified 10 high-confidence drug targets that included well-known oncogenes such as ERBB2 and RAF1, and novel oncogenes, notably KPNB1, which we investigated further...
August 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28811350/defining-the-dna-binding-site-recognized-by-the-fission-yeast-zn2cys6-transcription-factor-pho7-and-its-role-in-phosphate-homeostasis
#17
Beate Schwer, Ana M Sanchez, Angad Garg, Debashree Chatterjee, Stewart Shuman
Fission yeast phosphate homeostasis entails transcriptional induction of genes encoding phosphate-mobilizing proteins under conditions of phosphate starvation. Transcription factor Pho7, a member of the Zn2Cys6 family of fungal transcription regulators, is the central player in the starvation response. The DNA binding sites in the promoters of phosphate-responsive genes have not been defined, nor have any structure-function relationships been established for the Pho7 protein. Here we narrow this knowledge gap by (i) delineating an autonomous DNA-binding domain (DBD) within Pho7 that includes the Zn2Cys6 module, (ii) deploying recombinant Pho7 DBD in DNase I footprinting and electrophoretic mobility shift assays (EMSAs) to map the Pho7 recognition sites in the promoters of the phosphate-regulated pho1 and tgp1 genes to a 12-nucleotide sequence motif [5'-TCG(G/C)(A/T)xxTTxAA], (iii) independently identifying the same motif as a Pho7 recognition element via in silico analysis of available genome-wide ChIP-seq data, (iv) affirming that mutations in the two Pho7 recognition sites in the pho1 promoter efface pho1 expression in vivo, and (v) establishing that the zinc-binding cysteines and a pair of conserved arginines in the DBD are essential for Pho7 activity in vivoIMPORTANCE Fungi respond to phosphate starvation by inducing the transcription of a set of phosphate acquisition genes that comprise a phosphate regulon...
August 15, 2017: MBio
https://www.readbyqxmd.com/read/28811306/replication-and-validation-of-genetic-polymorphisms-associated-with-survival-after-allogeneic-blood-or-marrow-transplant
#18
Ezgi Karaesmen, Abbas A Rizvi, Leah Preus, Philip L McCarthy, Marcelo C Pasquini, Kenan Onel, Xiaochun Zhu, Stephen Spellman, Christopher A Haiman, Daniel O Stram, Loreall Pooler, Xin Sheng, Qianqian Zhu, Li Yan, Qian Liu, Qiang Hu, Amy Webb, Guy Brock, Alyssa I Clay-Gilmour, Sebastiano Battaglia, David Tritchler, Song Liu, Theresa Hahn, Lara E Sucheston-Campbell
Multiple candidate gene association studies of non-HLA single nucleotide polymorphisms (SNPs) and outcomes after blood or marrow transplant (BMT) have been conducted. We identified 70 publications reporting 45 SNPs in 36 genes significantly associated with disease-related mortality, progression-free survival, transplant-related mortality and/or overall survival after BMT. Replication and validation of these SNP associations were performed using DISCOVeRY-BMT, a well-powered genome-wide association study consisting of two cohorts, totaling 2,883 BMT recipients with AML, ALL or MDS and their HLA-matched unrelated donors, treated from 2000-2011 and reported to the CIBMTR...
August 15, 2017: Blood
https://www.readbyqxmd.com/read/28811299/twenty-years-of-menin-emerging-opportunities-for-restoration-of-transcription-in-men1
#19
Koen M A Dreijerink, Marc Timmers, Myles Brown
Since the discovery of the multiple endocrine neoplasia type 1 (MEN1) gene in 1997, elucidation of the molecular function of its protein product, menin, has been a challenge. Biochemical, proteomics, genetics and genomics approaches have identified various potential roles, which converge on gene expression regulation. The most consistent findings show that menin connects transcription factors and chromatin modifying enzymes, in particular the histone H3K4 methyltransferase complexes MLL1 and MLL2. Chromatin immunoprecipitation combined with next generation sequencing has enabled studying genome-wide dynamics of chromatin binding by menin...
August 15, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28811274/hypoxia-in-combination-with-muscle-contraction-improves-insulin-action-and-glucose-metabolism-in-human-skeletal-muscle-via-the-hif-1%C3%AE-pathway
#20
Sven W Görgens, Tim Benninghoff, Kristin Eckardt, Christian Springer, Alexandra Chadt, Anita Melior, Jakob Wefers, Andrea Cramer, Jørgen Jensen, Kåre I Birkeland, Christian A Drevon, Hadi Al-Hasani, Jürgen Eckel
Skeletal muscle insulin resistance is the hallmark of type 2 diabetes, and develops long before the onset of the disease. It is well accepted that physical activity improves glycemic control but the knowledge on underlying mechanisms mediating the beneficial effects remains incomplete. Exercise is accompanied by a decrease in intramuscular oxygen levels resulting in induction of HIF-1α. HIF-1α is a master regulator of gene expression and might play an important role in skeletal muscle function and metabolism...
August 15, 2017: Diabetes
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